The calculation of vortex method has been accelerated by using special-purpose computers, MDGRAPE-2 and MDGRAPE-3, respectively. The similar algorithm has been implemented and the improvement in speed of MDGRAPE-2 was 100 times while MDGRAPE-3 was 1000 times faster when compared with the ordinary PC Xeon 5160(3.0GHz) for N=10. In addition, the speed of MDGRAPE-3 was 25 times faster compared wit...

We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bond...

The present study discusses some numerical techniques on the simultaneous use of the Fast Multipole Method (FMM) and special-purpose computer (MDGRAPE-3) to make the impractically expensive calculation feasible without the loss of numerical accuracy. In the present calculations, the impingement of two identical inclined vortex rings has been studied, and the computation time has been reduced by...

Bluff body calculation was accelerated by using a special-purpose computer, MDGRAPE-2, that was exclusively designed for molecular dynamics simulations. The three main issues were solved regarding the implementation of the MDGRAPE-2 on vortex methods. These issues were the efficient calculation of the Biot-Savart and stretching equation, the optimization of the table domain, and the round-off e...

Large-scale molecular dynamics simulations of the high-pressure transformations of the xenon/water system were performed involving special purpose molecular dynamics machines. We investigated several systems of different sizes and geometry at the suitable simulational conditions (density, temperature, etc.), which are similar to the experiments conducted on the xenon hydrates. A binary mixture ...

of magnetic materials with MDGRAPE-2 B. G. Elmegreen R. H. Koch M. E. Schabes T. Crawford T. Ebisuzaki H. Furusawa T. Narumi R. Susukita K. Yasuoka The use of accelerator hardware for micromagnetics simulations is described, along with some initial results. The accelerator calculates the dipole interactions at 400 gigaflops, allowing large simulations to be performed with arbitrary geometries. ...

We have achieved a sustained calculation speed of 281 Tflops for the optimization of the 3-D structures of proteins from the X-ray experimental data by the Genetic Algorithm – Direct Space (GA-DS) method. In this calculation we used MDGRAPE-3, special-purpose computer for molecular simulations, with the peak performance of 752 Tflops. In the GA-DS method, a set of selected parameters which defi...